Unable to launch julia 1.6 - SSL and glibc issues

General Usage
1

I recently installed Julia 1.6 on a CentOS 7 cluster, but am unable to run it.

[affans@hpc ~]$ julia
ERROR: Unable to load dependent library /home/affans/julia-1.6.1/bin/../lib/julia/libjulia-internal.so.1
Message:/usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /home/affans/julia-1.6.1/bin/../lib/julia/libjulia-internal.so.1)

From the official 1.6 launch thread and some help on Slack, I was able to solve this issue. Turns out glibc libraries on the cluster are version 2.17 but Julia apparently requires 2.22. The issue is with the libstdc++.so.6 library. I fixed this by running

# for julia 1.6, the glibc libraries are too old so make sure to use the julia shipepd ones
export LD_LIBRARY_PATH=/home/affans/julia-1.6.1/lib/julia:$LD_LIBRARY_PATH

This made everything work and it was great for a few hours… until I tried git clone and it failed with a BADCERT_NOT_TRUSTED error. Digging a bit more, it wasn’t a git issue, but a more generic issue with ssl certificates… for example:

[affans@hpc ~]$ curl https://julialang.org/
curl: (60) Cert verify failed: BADCERT_NOT_TRUSTED
More details here: http://curl.haxx.se/docs/sslcerts.html

If I comment out the LD_LIBRARY_PATH export (so it goes back to system libraries), all the ssl errors go away. So why is it that when I use the Julia’s shipped version of glibc libraries, it clashes?

This stuff is way out of my domain so any help would be sincerely appreciated.

2

This is not correct, official binaries of Julia for x86_64 platforms require glibc 2.12.2, which is way older than what you have in your system. The library which is giving you troubles is libstdc++, not glibc.

3

I see. So what does the symbol GLIBCXX_3.4.20 mean? And why does switching to the Julia library break ssl?

Some extra information. The libstdc++.so.6 in my system (/usr/lib64) has these “strings” (not sure what this means). I don’t see GLIBC_3.4.20 in here… but still, I am confused to why other things are breaking if I switch to the Julia library. Is there a way to fix this? Maybe building from source?

[affans@hpc lib64]$ strings libstdc++.so.6 | grep GLIBC
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBC_2.3
GLIBC_2.2.5
GLIBC_2.14
GLIBC_2.4
GLIBC_2.3.2
GLIBCXX_DEBUG_MESSAGE_LENGTH
4

That indicates the minimum version of libstdc++ required to load the library: ABI Policy and Guidelines. You system’s libstdc++ gets up to 3.4.19, which corresponds to gcc 4.8.3. BTW, since this is on a cluster you likely have a way to load a module with a more recent gcc toolchain, the default one is often fairly old. Clearing up LD_LIBRARY_PATH before starting Julia is a good idea anyway.

I recommend editing LD_LIBRARY_PATH only to run Julia, don’t modify the rest of the system just for Julia.

5

Well, if I get rid of the LD_LIBRARY_PATH (where I append the Julia folder first in the order), that’s when the ssl issues start. As soon as I comment that now, the ssl issues go away. So it does seem that when using to Julia’s libstdc++ has something to do with it.

Is there a way to do:

I recommend editing LD_LIBRARY_PATH only to run Julia, don’t modify the rest of the system just for Julia.

I mean I have

export LD_LIBRARY_PATH=/home/affans/julia-1.6.1/lib/julia:$LD_LIBRARY_PATH

which makes Julia work, but like I said, it somehow clashes with ssl certificates. It would be nice for Julia to use it’s own libstdc++ while the rest of the system uses whatever is there is /usr/lib64

6

Start Julia with

LD_LIBRARY_PATH="" julia

and that’s it.

1 Like
7

Oh! That works. So I just commented out the entire export LD_LIBRARY_PATH from my bashrc file. Not sure why I had it in there (maybe for some other program? will have to see what breaks).

Okay, so when LD_LIBRARY_PATH = "" , and I type in julia, what version of libstdc++ does it use? Does it use the system one (unlikely since the minimum version is only 3.4.19) or does it use the one that itself shipped with? I am guessing the latter.

And ofcourse, other programs that use libstdc++ use the system one… since how would they be aware of the Julia one (unless I append it to LD_LIBRARY_PATH which I was doing and it was messing things up).

Ah, 30 minutes to learn linux… a lifetime to master.

8

The latter. Official binaries of Julia v1.6 come with libstdc++.so.6.0.26, which corresponds to GCC 9.1.

1 Like